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Makefile
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Makefile
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COMPILER = g++
CXXFLAGS = -std=c++17 -O3 -DNDEBUG
MYLIBS = -I ./include
SDSLLIBS = -I ~/include -L ~/lib
SDSLFLAGS = -lsdsl -ldivsufsort -ldivsufsort64
THREADFLAGS = -pthread
SRCDIR = src
INCLUDEDIR = include
BINDIR = bin
EXECS = $(BINDIR)/fix_reference_for_indexing $(BINDIR)/construct_index $(BINDIR)/rf_mapping $(BINDIR)/contig_assembly $(BINDIR)/summary_info
all: $(EXECS)
####
$(BINDIR)/fix_reference_for_indexing: $(SRCDIR)/fix_reference_for_indexing.cpp
$(COMPILER) $(CXXFLAGS) $(SRCDIR)/fix_reference_for_indexing.cpp -o $(BINDIR)/fix_reference_for_indexing
$(BINDIR)/construct_index: $(INCLUDEDIR)/genomeutil.hpp $(SRCDIR)/construct_index.cpp
$(COMPILER) $(CXXFLAGS) $(MYLIBS) $(SDSLLIBS) $(SRCDIR)/construct_index.cpp -o $(BINDIR)/construct_index $(SDSLFLAGS)
$(BINDIR)/rf_mapping: $(INCLUDEDIR)/genomeutil.hpp $(SRCDIR)/rf_mapping.cpp $(SRCDIR)/rf_mapping_lib.hpp
$(COMPILER) $(CXXFLAGS) $(MYLIBS) $(SDSLLIBS) $(SRCDIR)/rf_mapping.cpp -o $(BINDIR)/rf_mapping $(SDSLFLAGS) $(THREADFLAGS)
$(BINDIR)/contig_assembly: $(SRCDIR)/contig_assembly.cpp
$(COMPILER) $(CXXFLAGS) $(SRCDIR)/contig_assembly.cpp -o $(BINDIR)/contig_assembly
$(BINDIR)/summary_info: $(INCLUDEDIR)/genomeutil.hpp $(INCLUDEDIR)/bedpe_manager.hpp $(SRCDIR)/summary_info.cpp
$(COMPILER) $(CXXFLAGS) $(MYLIBS) $(SRCDIR)/summary_info.cpp -o $(BINDIR)/summary_info
clean:
rm -f $(EXECS)